MedWorm provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest medical blog items that have been tagged with 'database'. Sat, 03 Sep 2011 01:53:05 +0100 http://www.medworm.com/index.php?rid=5118646&cid=t_104849_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Findividualizing-the-fight-against-cancer%2F2011.08.10 You have heard it countless times, “The War on Cancer.” President Nixon announced it. The National Cancer Institute has spearheaded what TV and radio commercials always talk about as “the fight against cancer.” Singular. But we really need to start thinking about it as a plural.  Wars on cancer. Fights against cancer. Taking it one step further, we need to see each person’s fight as an individual battle.  Not just individualized to the patient’s spirit or age or sense of hope, but individualized to his or her particular biology, matched up with the specific cancer and available treatments. That is the nature of “personalized medicine” applied to cancer. We’ve been talking about it for a few years around here, but what’s exciting now is that even more super smart peopl... Better Health blogs http://www.medworm.com/rss/comments.php?id=5118646 Wed, 10 Aug 2011 18:00:06 +0100 5118646 http://www.medworm.com/index.php?rid=5077693&cid=t_104849_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Ffootball-helmets-which-ones-are-most-likely-to-prevent-head-injuries%2F2011.07.28 Courtesy of Virginia Tech-Wake Forest School of Biomedical Engineering and Sciences: National Impact Database Adult Football Helmet Ratings – May 2011 A total of 10 adult football helmet models were evaluated using the STAR evaluation system for May 2011 release.  All 10 are publicly available at the time of publication.  Helmets with lower STAR values provide a reduction in concussion risk compared to helmets with higher STAR values.  Based on this, the best overall rating of ‘5 Stars’ has the lowest STAR value.  Group rankings are differentiated by statistical significance. If you’re in the market to buy a loved one a football helmet, or just curious, go and have a look. It doesn’t take long, there are only 10 helmets on the list. Go to the list. I got to this from ESPN’... Better Health blogs http://www.medworm.com/rss/comments.php?id=5077693 Thu, 28 Jul 2011 12:00:20 +0100 5077693 http://www.medworm.com/index.php?rid=4997532&cid=t_104849_88_f&fid=38129&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Flifeinthefastlane%2FWZHV%2F%7E3%2FeGWyjEbJ2TY%2F We have just started the long process of cataloguing the LITFL image collection - currently standing at 120,000 prospectively consented images from the last 15 years. (Source: Life in the Fast Lane) Life in the Fast Lane blogs http://www.medworm.com/rss/comments.php?id=4997532 Sun, 03 Jul 2011 07:28:58 +0100 4997532 http://www.medworm.com/index.php?rid=4921555&cid=t_104849_113_f&fid=34634&url=http%3A%2F%2Fwww.emrandhipaa.com%2Femr-and-hipaa%2F2011%2F06%2F07%2Fyou-might-be-a-jabba-the-hutt-emr-if%2F Many long time readers of EMR and HIPAA will know I like to call big, bulky, old EMR software systems, Jabba the Hutt EMR. I think comparing these old legacy EMR software to Jabba the Hutt is a great comparison. For those that don’t know Star Wars that well (and I’m no expert), Jabba the Hutt was a very powerful figure. Although, over time he’d grown so big that he wasn’t very nimble (to say the least). So, despite his power and prestige, there was little to admire about him. Does that sound a bit like some legacy EMR software? They’re big and powerful figures in the industry. However, their software has grown to the point that it’s clunky and not very nimble. Getting something changed on it is difficult and it’s built on a platform that makes it h... EMR and HIPAA blogs http://www.medworm.com/rss/comments.php?id=4921555 Tue, 07 Jun 2011 17:48:25 +0100 4921555 http://www.medworm.com/index.php?rid=4841830&cid=t_104849_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F05%2F18%2Fhow-to-create-a-partial-ucsc-genome-mysql-database%2F File under: simple, but a useful reminder UCSC Genome Bioinformatics is one of the go-to locations for genomic data. They are also kind enough to provide access to their MySQL database server: mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A However, users are given fair warning to “avoid excessive or heavy queries that may impact the server performance.” It’s not clear what constitutes excessive or heavy but if you’re in any doubt, it’s easy to create your own databases locally. It’s also easy to create only the tables that you require, as and when you need them. As an example, here’s how you could create only the ensGene table for the latest hg19 database. Here, USER and PASSWD represent a local MySQL user and password with full privileg... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4841830 Wed, 18 May 2011 04:54:10 +0100 4841830 http://www.medworm.com/index.php?rid=4803007&cid=t_104849_86_f&fid=38272&url=http%3A%2F%2Flaikaspoetnik.wordpress.com%2F2011%2F05%2F08%2F3rd-call-for-submissions-for-medical-information-matters-tools-for-searching-the-biomedical-literature%2F It takes some doing to breathe life into “Medical Information Matters” (blog carnival about medical  information). A month ago I wrote a 2nd call for submissions post for this blog carnival. Unfortunately the next host, Martin Fenner, didn’t have time to finish a blog post and has come up with a new (interesting) variation on the theme [...] (Source: Laika's MedLibLog) Laika's MedLibLog blogs http://www.medworm.com/rss/comments.php?id=4803007 Sun, 08 May 2011 21:25:49 +0100 4803007 http://www.medworm.com/index.php?rid=4780346&cid=t_104849_109_f&fid=34750&url=http%3A%2F%2Fpsychcentral.com%2Fblog%2Farchives%2F2011%2F05%2F03%2Fwho-knew-no-networking-on-the-social-networking-site-facebook%2F Silly me. I was thinking that the social networking site currently named Facebook could prove to be an effective networking tool. I humbly admit that I am one of those media whores who friends New York Times journalists not so much so that I can get to know them and eventually invite them over to my home for a nice meal my husband can whip up, but so that I can pitch them a story via Facebook mail and save myself and the technology company for whom I do some publicity about four grand a year, the average cost of a sophisticated media database and press release distribution service. I’m cheap and I’m tacky. Yes I am. Proud of it! Is that why I’ve been placed on probation? Yes. A two-day probation. Like the kind I used to get in Catholic grade school when I couldn’t s... World of Psychology blogs http://www.medworm.com/rss/comments.php?id=4780346 Tue, 03 May 2011 18:00:13 +0100 4780346 http://www.medworm.com/index.php?rid=4709166&cid=t_104849_86_f&fid=38272&url=http%3A%2F%2Flaikaspoetnik.wordpress.com%2F2011%2F04%2F12%2Fpubmeds-sudden-death-averted-for-now%2F MEDLINE is the National Library of Medicine‘s (NLM) premier bibliographic database of citations from biomedical journals. The content of MEDLINE is available via commercial, fee-for-service MEDLINE vendors, like OVID. On June 26, 1997, Vice President Al Gore officially announced free MEDLINE access via PubMed. This was one of the consequences of  the Freedom of Information Act (FOIA), a federal law that allows [...] (Source: Laika's MedLibLog) Laika's MedLibLog blogs http://www.medworm.com/rss/comments.php?id=4709166 Tue, 12 Apr 2011 16:56:57 +0100 4709166 http://www.medworm.com/index.php?rid=4704586&cid=t_104849_86_f&fid=38272&url=http%3A%2F%2Flaikaspoetnik.wordpress.com%2F2011%2F04%2F12%2Fpubmeds-sudden-death-averted-for-now%2F MEDLINE is the National Library of Medicine‘s (NLM) premier bibliographic database of citations from biomedical journals. The content of MEDLINE is available via commercial, fee-for-service MEDLINE vendors, like OVID. On June 26, 1997, Vice President Al Gore officially announced free MEDLINE access via PubMed. This was one of the consequences of  the Freedom of Information Act (FOIA), a federal law that allows [...] (Source: Laika's MedLibLog) Laika's MedLibLog blogs http://www.medworm.com/rss/comments.php?id=4704586 Tue, 12 Apr 2011 16:56:57 +0100 4704586 http://www.medworm.com/index.php?rid=4605985&cid=t_104849_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FRltCYzZI5qs%2F Here’s the schedule for the Tools session we’re having on Friday at Asilomar. I hope to be able to post everyone’s slides after the meeting as well. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=4605985 Thu, 17 Mar 2011 15:00:13 +0100 4605985 http://www.medworm.com/index.php?rid=4450454&cid=t_104849_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F02%2F08%2F2462%2F The Nature stable of journals. A byword for quality, integrity, impact. Witness this recent offering from Nature Biotechnology: Bale, S. et al. (2011) MutaDATABASE: a centralized and standardized DNA variation database. Nature Biotechnology 29, 117–118 doi:10.1038/nbt.1772 Unfortunately, although it describes an open, public database, the article itself costs $32 to read without subscription (update: it’s freely available as of one day after this post). Not to be deterred, I went to investigate MutaDATABASE itself. The alarm bells began to ring right there on the index page (see screenshot, right). Could that be right? I tried several browsers, in case of a rendering problem. Same result – no contents. There seems to be something missing Clicking on some of the link... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4450454 Tue, 08 Feb 2011 13:10:50 +0100 4450454 http://www.medworm.com/index.php?rid=4405778&cid=t_104849_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Fcranberry-juice-for-urinary-tract-infections-evidence-is-still-lacking%2F2011.01.26 It always somewhat surprises me how some interventions never seem to die. One therapy that refuses to be put to rest, or even to be clarified, is the use of cranberry juice for urinary tract infections (UTIs). PubMed references go back to 1962, and there are over 100 references. Firm conclusions are still lacking. There is a reasonable, but incomplete, basic science behind the use of the cranberry juice for UTIs. E. coli , the most common cause of UTIs, causes infection in the bladder by binding to the uroepithelial cells. To do this, they make  fimbriae,  proteinaceous fibers on the bacterial cell wall. Fimbriae are adhesins that attach to specific sugar based receptors on uroepithelial cells. Think Velcro. Being able to stick to cells is an important virulence factor for bacteri... Better Health blogs http://www.medworm.com/rss/comments.php?id=4405778 Wed, 26 Jan 2011 22:00:51 +0100 4405778 http://www.medworm.com/index.php?rid=4322636&cid=t_104849_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FgRRZQti7WfU%2F New genomes from Microsporidia are on the way from the Broad Institute and other groups, and will be a boon to those working on these fascinating creatures. Microsporidia are obligate intracellular parasites of eukaryotic cells and many can cause serious disease in humans. Some parasitize worms and insects too. The evolutionary placement of these species in the fungi is still debated with recent evidence placing them as derived members of the Mucormycotina based on shared synteny (conserved gene order), in particular around the mating type locus.  There is still some debate as to where this group belongs in the Fungal kingdom, with their highly derived characteristics and long branches they are still make them hard to place.  The synteny-based evidence was another way to find a phyloge... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=4322636 Fri, 07 Jan 2011 19:24:01 +0100 4322636 http://www.medworm.com/index.php?rid=4294820&cid=t_104849_118_f&fid=34702&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Fmspblog%2F%7E3%2FjVexktE5C_U%2F Joint Commission has announced the appointment of a new Medical Director, an Internist from the University of Pennsylvania Health System, Ana Pujols-McKee, M.D. “In this role, Dr. McKee will represent The Joint Commission enterprise as she focuses on and develops policies and strategies for promoting patient safety and quality improvement in health care. Her specific responsibilities will include providing support to The Joint Commission’s Patient Safety Advisory Group; overseeing work related to the development of the Sentinel Event Policy, National Patient Safety Goals and Sentinel Event Alerts; supervising the Sentinel Event Database; and overseeing the functions of the Standards Interpretation Group and the Office of Quality Monitoring. Dr. McKee also will provide clinical gu... MSSPNexus Blog blogs http://www.medworm.com/rss/comments.php?id=4294820 Sun, 26 Dec 2010 13:25:38 +0100 4294820 http://www.medworm.com/index.php?rid=4190161&cid=t_104849_88_f&fid=38129&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Flifeinthefastlane%2FWZHV%2F%7E3%2FqGH6TAC-eno%2F Dealing with this exponentially growing information resource can be challenging, especially as we are increasingly want to share our knowledge, and invite comment from our peers....enter Today I Learnt That (TILT) is the brainchild of Jon Brassey of TRIP Database and TRIP Answers fame. (Source: Life in the Fast Lane) Life in the Fast Lane blogs http://www.medworm.com/rss/comments.php?id=4190161 Tue, 23 Nov 2010 06:41:52 +0100 4190161 http://www.medworm.com/index.php?rid=4119468&cid=t_104849_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FTon_fTEQfqs%2F As part of background in preparing a grant I ended up writing a few scripts to see the distribution of fungal species with ITS data in GenBank.  The whole spreadsheet of the data is public and available here and I walk you through the data generation and summary below. ITS (Internal Transcribed Spacer) is the typically used barcode for identifying fungi at the species level as it works for most (but not all) groups of Fungi. It falls between highly conserved nuclear rDNA genes (18S, 5.8S, 28S) but tends to be hypervariable making it a reasonable locus for identification of species since it tends to be unique between species but fairly unchanged among individuals from the same species. You can see a Map of the amplified region from Tom Brun’s site or info at Rytas Vilgalys’s ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=4119468 Fri, 29 Oct 2010 06:10:20 +0100 4119468 http://www.medworm.com/index.php?rid=4002967&cid=t_104849_109_f&fid=34750&url=http%3A%2F%2Fpsychcentral.com%2Fblog%2Farchives%2F2010%2F09%2F26%2Fevidence-based-treatments-for-children-teens%2F We talk a lot about the different types of research conducted in psychology that measure the effectiveness of various treatment methods. In fact, we publish daily news stories that cover a lot of new research findings every week. Some of the treatment research has to do with medications, some with psychotherapy, and some with other methods of treatment. But it’s all confusing and can be more than a little overwhelming. Take, for instance, the contradictory findings and results surrounding antidepressant medications. Some research says they are no better than sugar pills — placebos. Other research says they can be effective, but you just need to find the right one at the right dose. It’s hard to know what the research really says as a whole. Wouldn’t it be nice if th... World of Psychology blogs http://www.medworm.com/rss/comments.php?id=4002967 Sun, 26 Sep 2010 10:29:12 +0100 4002967 http://www.medworm.com/index.php?rid=3915213&cid=t_104849_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F08%2F30%2Fgeo-database-curation-lagging-behind-submission%2F GSE and GDS records in GEOmetadb by date I was reading an old post that describes GEOmetadb, a downloadable database containing metadata from the GEO database. We had a brief discussion in the comments about the growth in GSE records (user-submitted) versus GDS records (curated datasets) over time. Below, some quick and dirty R code to examine the issue, using the Bioconductor GEOmetadb package and ggplot2. Left, the resulting image – click for larger version. Is the curation effort keeping up with user submissions? A little difficult to say, since GEOmetadb curation seems to have its own issues: (1) why do GDS records stop in 2008? (2) why do GDS (curated) records begin earlier than GSE (submitted) records? library(GEOmetadb) library(ggplot2) # update database if required usi... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3915213 Mon, 30 Aug 2010 08:11:16 +0100 3915213 http://www.medworm.com/index.php?rid=3902900&cid=t_104849_87_f&fid=39187&url=http%3A%2F%2Fgetbetterhealth.com%2Fa-truly-useful-emr%2F2010.08.25 I love computers. Really, I do. Despite my oft-repeated claims about the shortcomings of electronic medical records in their current form, I do believe that information technology has the potential to be of great help to me and other physicians in providing quality care to Americans. Stop laughing. I really mean it. I do not believe, however, that IT best serves the medical needs of our patients when used to create non-interactive silos of information sequestered in the offices and clinics of individual doctors. Even hospitals and large integrated health systems information remains stuck within that system, providing limited utility when patients travel, or even go to a doctor not affiliated with the system. Although some (especially in government) seem to feel that expanding those kinds o... Better Health blogs http://www.medworm.com/rss/comments.php?id=3902900 Wed, 25 Aug 2010 16:00:29 +0100 3902900 http://www.medworm.com/index.php?rid=3845238&cid=t_104849_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F08%2F09%2Fmongodb-mongoid-and-mapreduce%2F I’ve been experimenting with MongoDB’s map-reduce, called from Ruby, as a replacement for Ruby’s Enumerable methods (map/collect, inject). It’s faster. Much faster. Next, the details but first – the disclaimers: My database is not optimised (using, e.g. indices) My non-map/reduce code is not optimised; I’m sure there are better ways to perform database queries and use Enumerable than those in this post My map/reduce code is not optimised – these are my first attempts In short nothing is optimised, my code is probably awful and I’m making it up as I go along. Here we go then! The Mongoid models A couple of posts ago, I outlined a Rails application to store feeds and entries from FriendFeed. Here are the models, with fields and methods remov... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3845238 Mon, 09 Aug 2010 08:12:19 +0100 3845238 http://www.medworm.com/index.php?rid=3718624&cid=t_104849_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F07%2F02%2Fhow-many-monotypic-genera%2F During all the recent discussion around Neandertals and modern humans, it’s often pointed out that Homo sapiens is the sole extant representative of the genus Homo. I began to wonder “how unusual is this?” in a FriendFeed comment thread. What resources exist that could help us to answer this question? Genera that contain only one species are termed monotypic. Wikipedia even has a category page for this topic but their lists are limited, since Wikipedia is not a comprehensive taxonomy resource. Taxonomy is not my specialty but once in a while, I enjoy challenging myself with unfamiliar resources and data types. I figured initially that we could get some way towards an answer using BioSQL and the NCBI taxonomy database. As it turned out I was completely wrong, but it was an... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3718624 Fri, 02 Jul 2010 02:56:59 +0100 3718624 http://www.medworm.com/index.php?rid=3710720&cid=t_104849_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FHmUqNNb51wE%2F I’ll indulge a bit here to happily to point to the cover of this week’s PNAS with an image of Coprinopsis cinerea mushrooms fruiting referring to our article on the genome sequence of this important model fungus.  You should also enjoy the commentary article from John Taylor and Chris Ellison that provides a summary of some of the high points in the paper. Stajich, J., Wilke, S., Ahren, D., Au, C., Birren, B., Borodovsky, M., Burns, C., Canback, B., Casselton, L., Cheng, C., Deng, J., Dietrich, F., Fargo, D., Farman, M., Gathman, A., Goldberg, J., Guigo, R., Hoegger, P., Hooker, J., Huggins, A., James, T., Kamada, T., Kilaru, S., Kodira, C., Kues, U., Kupfer, D., Kwan, H., Lomsadze, A., Li, W., Lilly, W., Ma, L., Mackey, A., Manning, G., Martin, F., Muraguchi, H., Natvig, D.,... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=3710720 Tue, 29 Jun 2010 17:35:11 +0100 3710720 http://www.medworm.com/index.php?rid=3385311&cid=t_104849_86_f&fid=38272&url=http%3A%2F%2Flaikaspoetnik.wordpress.com%2F2010%2F03%2F20%2Fan-evidence-pyramid-that-facilitates-the-finding-of-evidence%2F Earlier I described that there are so many search- and EBM-pyramids that it is confusing. I described  3 categories of pyramids: Search Pyramids Pyramids of EBM-sources Pyramids of EBM-levels (levels of evidence) In my courses where I train doctors and medical students how to find evidence quickly, I use a pyramid that is a mixture of 1. and 2. [...] (Source: Laika's MedLibLog) Laika's MedLibLog blogs http://www.medworm.com/rss/comments.php?id=3385311 Sat, 20 Mar 2010 15:27:17 +0100 3385311 http://www.medworm.com/index.php?rid=3362443&cid=t_104849_109_f&fid=38954&url=http%3A%2F%2Ffrontierpsychiatrist.co.uk%2Fnhs-summary-care-record%2F People living in London and four other strategic health authorities are currently receiving information in the post about the rollout of the NHS Summary Care Record (SCR) system.  SCR is part of the NHS Care Records System, a large UK government IT project which aims for more effective sharing of patient records between NHS services.  When the system is in full swing, NHS staff in Newcastle (say) will be able to access the medical records of someone requiring care whose residence and GP is in Penzance.  The SCR will initially contain records of such things as medications and allergies, but may eventually become more detailed and also allow access to specialists’ letters and scans. Controversy about this centralised system has been rumbling on for some time and before you read further ... blogs http://www.medworm.com/rss/comments.php?id=3362443 Fri, 12 Mar 2010 19:33:54 +0100 3362443 http://www.medworm.com/index.php?rid=3223443&cid=t_104849_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F01%2F30%2Fphosphogrid%2F I no longer work on protein kinases but when I did, PhosphoGRID is the kind of database that I would have wanted to see. It features: A nice clean interface, with good use of Javascript Useful information returned from a simple search form Data for download in plain text format with no restrictions or requirements for registration All it lacks is a RESTful API, but nothing is perfect :-) Published in the little-known but often-useful journal Database: PhosphoGRID: a database of experimentally verified in vivo protein phosphorylation sites from the budding yeast Saccharomyces cerevisiae. doi:10.1093/database/bap026. Filed under: bioinformatics, publications, web resources Tagged: database, phosphory, protein kinases (Source: What You're Doing Is Rather Desperate) What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3223443 Sat, 30 Jan 2010 04:10:45 +0100 3223443 http://www.medworm.com/index.php?rid=3153558&cid=t_104849_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F01%2F08%2Fsamples-per-seriesdataset-in-the-ncbi-geo-database%2F Andrew asks: I want to get an NCBI GEO report showing the number of samples per series or data set. Short of downloading all of GEO, anyone know how to do this? Is there a table of just metadata hidden somewhere? At work, we joke that GEO is the only database where data goes in, but it won’t come out. However, there is an alternative: the GEOmetadb package, available from Bioconductor. The R code first, then some explanation: # install GEOmetadb source("http://bioconductor.org/biocLite.R") biocLite("GEOmetadb") library(GEOmetadb) # connect to database getSQLiteFile() con <- dbConnect(SQLite(), "GEOmetadb.sqlite") # count samples per GDS gds.count <- dbGetQuery(con, "select gds,sample_count from gds") gds.count[1:5,] # first 5 results... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3153558 Fri, 08 Jan 2010 01:01:09 +0100 3153558 http://www.medworm.com/index.php?rid=3149253&cid=t_104849_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F01%2F07%2Fhow-to-archive-data-via-an-api-using-ruby-and-mongodb%2F I was going to title this post “How to: archive a FriendFeed feed in MongoDB”. The example code does just that but (a) I fear that this blog suggests a near-obsession with FriendFeed (see tag cloud, right sidebar) and (b) the principles apply to any API that returns JSON. There are rare examples of biological data with JSON output in the wild, e.g. the ArrayExpress Gene Expression Atlas. So I’m still writing a bioinformatics blog ;-) Let’s go straight to the code: #!/usr/bin/ruby require "rubygems" require "mongo" require "json/pure" require "open-uri" # db config db = Mongo::Connection.new.db('friendfeed') col = db.collection('lifesci') # fetch json 0.step(9900, 100) {|n| f = open("http://friendfeed-api.com/v2/feed/... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3149253 Thu, 07 Jan 2010 00:17:46 +0100 3149253 http://www.medworm.com/index.php?rid=2927462&cid=t_104849_125_f&fid=36046&url=http%3A%2F%2Fdentistrylibrary.blogspot.com%2F2009%2F10%2Finformit-health-to-replace-meditext.html Informit Health Collection is now available on our database trials page. The Informit Health Collection will deliver instant cover-to-cover access to core allied health information from the Australasian region. Many of the peer reviewed journal titles it includes are uniquely available through Informit, offering new perspectives of benefit to allied health professionals and students. As with other Informit databases, the Collection also provides access to grey literature such as conference proceedings and reports that are often difficult to locate. Informit Health Collection will replace Meditext on 1 January 2010.  Subscribe in a reader (Source: DentistryLibrary@Sydney) DentistryLibrary@Sydney blogs http://www.medworm.com/rss/comments.php?id=2927462 Mon, 26 Oct 2009 01:15:00 +0100 2927462 http://www.medworm.com/index.php?rid=2772554&cid=t_104849_107_f&fid=36672&url=http%3A%2F%2Fwww.sciencebase.com%2Fscience-blog%2F50-million-chemicals.html Chemical Abstracts Service (CAS) will announce the 50 millionth registered chemical substance in its Registry, tomorrow (8th September). According to the email I received from a CAS spokesman, “The number itself represents an important milestone both for researchers and CAS, but even more significant is the pace of scientific discovery around the world.” Roger Schenck, Manager of the Content Planning Department at CAS, adds that, “More scientific literature is being published and we have noticed an explosive growth of patent literature since 1998 that accounts for the rapid growth of substance information available.” By contrast, it took 33 years for CAS to register 10 million compounds, a milestone reached in 1990. It’s intriguing to think that two decades af... Sciencebase Science Blog blogs http://www.medworm.com/rss/comments.php?id=2772554 Mon, 07 Sep 2009 12:00:48 +0100 2772554 http://www.medworm.com/index.php?rid=2712228&cid=t_104849_125_f&fid=36046&url=http%3A%2F%2Fdentistrylibrary.blogspot.com%2F2009%2F08%2Fnew-dentistry-oral-health-database.html Dentistry & Oral Sciences Source™ is a new database which indexes dentistry and oral sciences journals commonly purchased by dental schools and other related institutions. It also includes a collection of important full-text journals including many of the top ranked titles in the discipline, as well as dozens of e-books.The Library has organized a 60 days trial of this database. Click here for more information and to access Dentistry & Oral Sciences Source. The trial will end in early October. Subscribe in a reader (Source: DentistryLibrary@Sydney) DentistryLibrary@Sydney blogs http://www.medworm.com/rss/comments.php?id=2712228 Tue, 18 Aug 2009 01:52:00 +0100 2712228 http://www.medworm.com/index.php?rid=2512112&cid=t_104849_125_f&fid=36046&url=http%3A%2F%2Fdentistrylibrary.blogspot.com%2F2009%2F06%2Fexciting-new-3d-interactive-resource.html The Library has organized a trial of 3D Head and Neck Anatomy for Dentistry on Anatomy.tv To access this interactive resource go to databases and scroll down to Anatomy.tvPlease try it out and let us know what you think using the Database Evaluation Form. Your comments are vital to the overall evaluation process and will have an important influence on whether the Library will subscribe to this resource. The trial is running until the end of June. Subscribe in a reader (Source: DentistryLibrary@Sydney) DentistryLibrary@Sydney blogs http://www.medworm.com/rss/comments.php?id=2512112 Tue, 16 Jun 2009 03:51:00 +0100 2512112 http://www.medworm.com/index.php?rid=2389916&cid=t_104849_109_f&fid=34795&url=http%3A%2F%2Fsoloshrink.blogspot.com%2F2009%2F05%2Fanother-electronic-medical-record.html I have harped on the topics of the potentially disastrous consequences of data loss or theft from medical health database repositories for some time now. I have personally been the victim of such a data loss by the Veteran's Health Administration, which lost all my provider information, financial account and license numbers, social security and business banking numbers, addresses, and all the other personal information to make identity theft a breeze. Nothing awful happened as a result of this loss. I was given a year's free three bureau credit monitoring subscription by the VHA. It is my personal belief that one of their less experienced employees or interns had simply carried the information for a service provider demographic study offsite on a thumb drive to work on it at home and lost... Solo Shrink blogs http://www.medworm.com/rss/comments.php?id=2389916 Thu, 07 May 2009 05:37:00 +0100 2389916 http://www.medworm.com/index.php?rid=2260157&cid=t_104849_132_f&fid=37823&url=http%3A%2F%2Fathena.bioc.uvic.ca%2Fnode%2F966 Check out STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) database of known and predicted protein interactions. Search for your favorite protein interactions, direct (physical) and indirect (functional) on this database! (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=2260157 Fri, 13 Mar 2009 06:33:05 +0100 2260157 http://www.medworm.com/index.php?rid=2260108&cid=t_104849_131_f&fid=35005&url=http%3A%2F%2Ffeedproxy.google.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2FYGrts5CFiSk%2F Shepard Fairley has gotten alot of notice lately for his Obama art that has been replicated pretty much everywhere. I mocked up a homage to his earlier street art — here we’ll discuss the growing Aspergillus genome posse. But the work from mainly the JCVI, Broad Institute, JGI, NITE, and Sanger centre has generated an excellent collection of genome sequences for the Eurotiales clade (feel free to get a login for the wiki and add other that are missing).  The Aspergillus community now has a AGD - Aspergillus Genome Database project that includes a curator of genome annotation (they are hiring) and presumably literature in the SGD and CGD model of curation. I think a lot of other projects have a Posse too (or maybe just a loosely organized band) in terms of a community of peop... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2260108 Thu, 12 Mar 2009 18:09:35 +0100 2260108 http://www.medworm.com/index.php?rid=2243024&cid=t_104849_132_f&fid=37823&url=http%3A%2F%2Fathena.bioc.uvic.ca%2Fnode%2F952 The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data.  UniProt provides the scientific community with a protein knowledgebase (UniProtKB), sequence clusters (UniRef), sequence archive (UniParc), and supporting data consisting of literature citations, taxonomy, keywords and more. (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=2243024 Sat, 07 Mar 2009 02:16:04 +0100 2243024 http://www.medworm.com/index.php?rid=2196280&cid=t_104849_132_f&fid=37823&url=http%3A%2F%2Fathena.bioc.uvic.ca%2Fnode%2F929 David Leader and James Milner-White, of the Faculty of Biomedical and Life Sciences in the University of Glasgow have built a freely accessible web application called Motivated Proteins.  This web facility was designed for protein scientists in mind to study small three-dimensional motifs without requiring knowledge of either Structured Query Language or the underlying database schema.  Their study has been published in BMC Bioinformatics, February 2009, entitled Motivated Proteins: A web application for studying small three-dime read more (Source: VBRC Blog) VBRC Blog blogs http://www.medworm.com/rss/comments.php?id=2196280 Thu, 19 Feb 2009 04:47:05 +0100 2196280 http://www.medworm.com/index.php?rid=2177560&cid=t_104849_131_f&fid=35005&url=http%3A%2F%2Ffungalgenomes.org%2Fblog%2F2009%2F02%2Fntetrasperma-ndiscreta%2F The JGI in collaboration with our lab at Berkeley have released the Neurospora tetrasperma (mat A) and N. discreta (mat A) genome sequences and annotation after about two years of work.  These are two closely related species to the well studied laboratory workhorse Neurospora crassa. The N.tetrasperma assembly (8X) has an N50 of 976kb and is highly colinear with the N.crassa genome.  With the JGI, we’ve also done some additional 454 sequencing which will represent an improved assembly and 23X coverage in the next release.  We also did some comparative scaffolding and can basically double that N50 - most of which looks good when compared to the improved V2 assembly. The N.discreta assembly (8X) is also quite good with an N50 of 2.3 Mb. For comparison, the V7 of N.crassa has an N50 ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2177560 Wed, 11 Feb 2009 07:08:50 +0100 2177560 http://www.medworm.com/index.php?rid=2671090&cid=t_104849_147_f&fid=38831&url=http%3A%2F%2Frenshaw01.wordpress.com%2F2009%2F02%2F06%2Fa-look-at-free-medical-and-scientific-search-tools%2F I used to use the same little stable of search engines to find what I need on the Web (such as PubMed, Journalseek, a metasearch engine, occasionally Google…). But now I’ve been turned on to a host more search engines that are sweet to use, easier on the eye and deliver as good, if not better, results. Why bother looking into search engines? There is no denying it, Web 2.0 has changed the way we use the Internet. We spend more time on-line because more of our resources are on-line. With more resources on-line, there is more to filter through to find our chosen nuggets of vital information. Therefore, tools that make searching easier and faster have got to be a bonus. Search engines are not infallible. They will miss some sites and some articles. To ensure that we’ve done the best sea... Medical Communicating blogs http://www.medworm.com/rss/comments.php?id=2671090 Fri, 06 Feb 2009 20:58:26 +0100 2671090 http://www.medworm.com/index.php?rid=2147612&cid=t_104849_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F527593699%2F I’m working to make more data available in the genome browsers for fungi. One is adding in the Primer information from the Neurospora KO project to the Neurospora browser to indicate the position and primer sequences for all the gene knockouts being (or already) constructed.  At least 60% of the genes have been knocked out and are available from the FGSC. We’re also integrating SNP data using the HapMap glyphs in which you can see one way to view this information in the Genome Browser for Coccidioides.  Working on other information including PhastCons conservation profiles and other information in our development server and hope to make this public soon. © Jason Stajich for The Hyphal Tip, 2009. | Permalink | No comment Add to del.icio.us Search blogs linking... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2147612 Fri, 30 Jan 2009 22:12:54 +0100 2147612 http://www.medworm.com/index.php?rid=2147678&cid=t_104849_125_f&fid=36046&url=http%3A%2F%2Fdentistrylibrary.blogspot.com%2F2009%2F01%2Fdatabase-on-trial.html The following database is currently on trial at the University of Sydney Library.Biomedical & Life Sciences Collection - Trial ends 27th of February, 2009. You will need to login with your UniKey to obtain a password.The Biomedical & Life Sciences Collection contains over 900 online audio-visual seminar style talks, each especially commissioned from leading world experts. It is of interest across many disciplines and will appeal to researchers, lecturers, graduate students and advanced undergraduates in biomedical and life sciences. The resource is organised into comprehensive animated audiovisual presentations and is regularly expanded and updated. To find talks matching your interests browse the series or use the search facility. A keyword search for 'dental' finds dental anatomy, dental... DentistryLibrary@Sydney blogs http://www.medworm.com/rss/comments.php?id=2147678 Thu, 29 Jan 2009 06:23:00 +0100 2147678 http://www.medworm.com/index.php?rid=2121796&cid=t_104849_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F519249058%2F The Broad Institute in collaboration with many of the Coprinopsis cinereus (Coprinus cinerea) community of researchers have updated the genome annotation for C. cinereus with additional gene calls based on ESTs and improved gene callers. The annotation was made on the 13 chromosome assembly produced by work by SEMO fungal biology group and collaborators across the globe including a BAC map from H. Muraguchi.  Thanks to Jonathan Goldberg and colleagues at the Broad Institute for getting this updated annotation out the door.   This updated annotation is able to join and split several sets of genes and the gene count sits at just under 14k genes in this 36Mb genome. There are a couple of hiccups in the GTF and Genome contig/supercontig file naming that I am told will be fixed by early next ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2121796 Thu, 22 Jan 2009 00:42:40 +0100 2121796 http://www.medworm.com/index.php?rid=2095831&cid=t_104849_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F01%2F11%2Feasy-visualisation-of-database-schemas-using-sqlfairy%2F BioSQL schema Here’s a common problem solved: how to generate a pretty picture of your database schema. A Google search throws up all manner of home-brewed solutions using graphviz, perl scripts and so on. Or you can make life easier and simply install SQLFairy. Under Ubuntu: as simple as “sudo apt-get install sqlfairy”. Next, dump your database tables, e.g. for MySQL: mysqldump -u username -p -d mydatabase > mydatabase.sql Finally, for a PNG image of your schema: sqlt-graph -f MySQL -o mydatabase.png -t png mydatabase.sql Too easy. Example shown is the BioSQL schema. update: if your schema lacks explicit foreign keys, try the –natural-join options (man sqlt-graph, man sqlt-diagram) Posted in bioinformatics, computing, linux, research diary  &nbsp... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2095831 Sun, 11 Jan 2009 08:45:44 +0100 2095831 http://www.medworm.com/index.php?rid=2089910&cid=t_104849_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F01%2F09%2Fwords-fail-me%2F As I’m a biologist, rather than an inorganic chemist or a mineralogist, I don’t have much (well, any) need to look at crystal structures of simple inorganic compounds. Just as well… …our story begins at Twitter, where David Bradley asks: Anyone know where to find crystal structures of sodium hypochlorite and sodium bisulfate (cif files or similar) ? #science #crystal Never thought about it, you say, but surely it can’t be very difficult. So you head to Google and try searches such as “inorganic crystal structure database”. Where you unearth two main players: the Inorganic Crystal Structure Database (ICSD) and the Cambridge Structural Database (CSD). Both are private, requiring registration, login and in one case, installation of an X-client. Comi... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=2089910 Fri, 09 Jan 2009 04:28:54 +0100 2089910 http://www.medworm.com/index.php?rid=2076959&cid=t_104849_88_f&fid=38129&url=http%3A%2F%2Fsandnsurf.medbrains.net%2F2008%2F12%2Ftop-8-bedside-health-search-engines-2008%2F Mednar has just been voted the ‘clear number one‘ by Medical librarian and author - Hope Leman (writing for AltSearchEngines.com) in her Top 10 Health Search Engines of 2008. My list is based on ‘rapid resolution’ at the bedside (or at least pretty close to it!). Needing to find answers to clinical questions, guidelines, images to demonstrate signs [...] (Source: Life in the Fast Lane) Life in the Fast Lane blogs http://www.medworm.com/rss/comments.php?id=2076959 Tue, 30 Dec 2008 07:40:24 +0100 2076959 http://www.medworm.com/index.php?rid=2027166&cid=t_104849_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F479999669%2F A new and improved annotation of Cryptococcus neoformans var grubii strain H99 (serotype A) has been made available in GenBank and the Broad Institute website. This update is collaboration between several groups providing data and analyses and the genome annotation team at the Broad Institute. Some changes noted by the Broad Institute include: “This release of gene predictions for the serotype A isolate Cryptococcus neoformans var. grubii H99 is based on a new genomic assembly provided by Dr. Fred Dietrich at the Duke Center for Genome Technology. The new assembly consists of 14 nuclear chromosomes and a single 21 KB mitochondrial chromosome, and has resulted in a reduction of the estimated genome size from 19.5 to 18.9 Mb. Improvements in the assembly and in our annotation process h... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=2027166 Tue, 09 Dec 2008 23:18:06 +0100 2027166 http://www.medworm.com/index.php?rid=2011192&cid=t_104849_133_f&fid=35096&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FAutismVox%2F%7E3%2FYUR4HtQYKtc%2F Via Cynthia Samuels On Special Education blog at EdWeek, I found this Autism Legislation Database on the National Conference of States Legislatures website. You can also access a state-by-state database on autism legislation here. Tags: asd, asperger, autism, autism blog, database, disabilities blog, disability, Education, Health, Insurance, Legislation, policy, statesShare This (Source: Autism Vox) Autism Vox blogs http://www.medworm.com/rss/comments.php?id=2011192 Wed, 03 Dec 2008 23:01:14 +0100 2011192 http://www.medworm.com/index.php?rid=1853649&cid=t_104849_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F412456461%2F A paper (Park et al, BMC Genomics) from Fungal Bioinformatics Lab at Seoul University in South Korea describes their new "Fungal P450 Database". The database contains sequence, names, and genome links for P450's (or Cytochrome P450s) identified by similarity and phylogenetic classification from genome annotations.  The group is using most of annotated genomes in GenBank (and I think some from elsewhere) of bacterial, fungi, animals, and plants. I find the current nomenclature for this family of genes confusing but it has been I am sure a difficult job and wrangled to a large part by David Nelson (who also has a new paper on the CYPome of Aspergillus nidulans). I have found it difficult to follow the logic for naming these members, as it didn't seem to be particularly phylogenetic a... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1853649 Mon, 06 Oct 2008 04:43:33 +0100 1853649 http://www.medworm.com/index.php?rid=1847987&cid=t_104849_133_f&fid=35096&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FAutismVox%2F%7E3%2Fl6p7i7M-uFI%2F As the October 1st issue of Scientific American Mind reminds us, words have power. I know this even more whenever I hear my son Charlie speak. He was very, very late to talk and he first didn’t talk at all, but used sign language. Today he speaks in short phrases and sentences, and almost-sentences. A lot of words get thrown around about autism on the Internet, on blogs and newspaper and media websites and who knows where else. Too often, even most often, it seems that the vast percentage of those words are in the realm of misinformation, as the numerous mentions of notions about what causes autism, from power plants in Texas to the quite infamous hypotheses about vaccines and/or mercury. As Dr. Paul Offit noted on his Science Blogs Book Club post today: A couple of bloggers praised ... Autism Vox blogs http://www.medworm.com/rss/comments.php?id=1847987 Thu, 02 Oct 2008 23:29:28 +0100 1847987 http://www.medworm.com/index.php?rid=1826914&cid=t_104849_105_f&fid=36987&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FIvorKovicMd%2F%7E3%2F397498729%2F PubSearch is an application for the iPhone designed to search Pubmed. It has a simple user interface and is pretty fast. Developers have already announced the enhanced version of this app, called PubSearchPlus which will offer more features. (Source: Ivor Kovic, M.D.) Ivor Kovic, M.D. blogs http://www.medworm.com/rss/comments.php?id=1826914 Fri, 19 Sep 2008 19:51:59 +0100 1826914 http://www.medworm.com/index.php?rid=1785941&cid=t_104849_113_f&fid=34933&url=http%3A%2F%2Fpalmdoc.net%2F%3Fp%3D1777 Like iSilo, Handbase is one of the “must have” applications for PDAs/Smartphones. It is an excellent portable database manager and one can keep plenty of useful bits of information. I for one use it to keep chemotherapy regimens, charge code lists and other databases I use in my daily practice. There are also medical applets/databases you can download from the Handbase Gallery. The good news for iPhone users is that DDHSoftware plan to release a version for the iPhone and in fact you can take a sneak peak right here a Coming soon: Handbase for the iPhone (Source: The Palmdoc Chronicles) The Palmdoc Chronicles blogs http://www.medworm.com/rss/comments.php?id=1785941 Wed, 10 Sep 2008 04:00:00 +0100 1785941 http://www.medworm.com/index.php?rid=1750129&cid=t_104849_132_f&fid=35028&url=http%3A%2F%2Flurena.vox.com%2Flibrary%2Fpost%2Fdecipher.html%3F_c%3Dfeed-rss The Database of Chromosomal Imbalance and Phenotype in Humans using Ensembl Resources Nigel Carter Morning Session, 2 September (11th MGED Meeting, 1-4 September, 2008) Genomic disorders, e.g. Down's Syndrome (3 copies of chromosome 21). Need gen... Read and post comments | Send to a friend (Source: Systems Biology & Bioinformatics) Systems Biology & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=1750129 Tue, 02 Sep 2008 09:35:39 +0100 1750129 http://www.medworm.com/index.php?rid=1734162&cid=t_104849_125_f&fid=36046&url=http%3A%2F%2Fdentistrylibrary.blogspot.com%2F2008%2F08%2Fdatabase-on-trial.html The following database is currently on trial at the University of Sydney Library. Please try it out and let us know what you think using the the database evaluation form below.Clin-eguide (Ovid) trial - Trial ends 30th of September, 2008Clin-eguide is a one-stop evidence based resources searching tool for Dentistry, Pharmacy, Medical and allied health students and staff.It integrates clinically relevant, evidence-based information resources from diagnostic and treatment guidelines to drug description and natural product reviews, and delivers it quickly and easily to the point of care. This, coupled with the ability to access the primary source literature, allows user access to a comprehensive research tool.Make sure you look at:• Visual DX- access to 16,000 images that can help diagnose ... DentistryLibrary@Sydney blogs http://www.medworm.com/rss/comments.php?id=1734162 Tue, 26 Aug 2008 06:59:00 +0100 1734162 http://www.medworm.com/index.php?rid=1658166&cid=t_104849_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F347809614%2F Report concludes that a fungal genome database is of "the highest priority". This is the title as listed in PubMed for this article from Future Medicine about the AAM report on charting future needs and avenues of research on the fungal kingdom. The need for a comprehensive database for information about fungi, starting at least with systematic collections of genomic and transcript data, is highlighted as a major need.  Really and sort of new database effort should strive to be more comprehensive and include genetic and population data (alleles, strains) and information like protein-protein, protein-nucleic acid interactions (as Pedro mentioned). But on top of that it, it needs to be comparative so that information from systems that serve as great models can be transferred to other fungal... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1658166 Sun, 27 Jul 2008 23:01:00 +0100 1658166 http://www.medworm.com/index.php?rid=1603096&cid=t_104849_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F331008458%2F The American Academy of Microbiology has released a report (PDF) on the Fungal Kingdom outlining importance of research in the kingdom and recommending several areas of priority for future areas of research. One recommendation that makes the top of the list is an integrated database for fungal genomes, something we're keenly interested in seeing happen.  This sort of centralized repository of functional annotation, literature links, and genome sequences and annotation is critical given the 150+ genomes that are available or on their way.  Systematic re-annotation with consistent tools, comparative analyses and gene predictions, and linking gene sequences by homology and ortholog predictions are a critical component to fully utilizing the genomic data that has been produced for the fungi ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1603096 Wed, 09 Jul 2008 18:49:15 +0100 1603096 http://www.medworm.com/index.php?rid=1475140&cid=t_104849_111_f&fid=34834&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FMentalNurse%2F%7E3%2F299043945%2F Conclusions Serious events, as indicated by a hospital admission or death, are frequent following the short-term use of antipsychotic drugs in older adults with dementia. Antipsychotic drugs should be used with caution even when short-term therapy is being prescribed.” The report is obviously skewed in as far as the three groups studied for the report were not randomised so the increased mortality and admission rates may have been due to the underlying psychopathology. Those not receiving anti psychotics were also presumably fitter and healthier on average that the people in the other groups but the results do beg the question should we be using these drugs at all with elderly confused patients especially if the drugs are being used as a substitute for adequate nursing care? (Source: Men... Mental Nurse blogs http://www.medworm.com/rss/comments.php?id=1475140 Tue, 27 May 2008 11:47:46 +0100 1475140 http://www.medworm.com/index.php?rid=1466453&cid=t_104849_105_f&fid=36987&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FIvorKovicMd%2F%7E3%2F296848963%2F PubMed provides access to Medline, a premier bibliographic database that contains references to journal articles in the life sciences with a concentration on biomedicine. It is available via the NCBI Entrez retrieval system, which was developed by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM), located at the U.S. National Institutes of Health (NIH).  PubMed is extremely popular among biomedical researchers, in part because it offers free access, contrary to other such search engines like Scopus and Web of Science. However, during the years I heard a lot of people complaining about PubMed. They do not like its interface and are not satisfied with search results it provides. A lot of these people never gave any thought about PubMed, nor d... Ivor Kovic, M.D. blogs http://www.medworm.com/rss/comments.php?id=1466453 Fri, 23 May 2008 23:28:53 +0100 1466453 http://www.medworm.com/index.php?rid=1436934&cid=t_104849_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F288882594%2F The Trichoderma reesei genome paper was recently published in Nature Biotechnology from Diego Martinez at LANL with collaborators at JGI, LBNL, and others. This fungus was chosen for sequencing because it was found on canvas tents eating the cotton material suggesting it may be a good candidate for degrading cellulose plant material as part of cellulosic ethanol or other biofuels production.  The fungus also has starring roles in industrial processes like making stonewashed jeans due to its prodigious cellulase production. The most surprising findings from the paper include the fact that there are so few members of some of the enzyme families even though this fungus is able to generate enzymes with so much cellulase activity. The authors found that there is not a significantly larger numb... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1436934 Mon, 12 May 2008 19:27:46 +0100 1436934 http://www.medworm.com/index.php?rid=1368869&cid=t_104849_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F269197633%2F Ewan Birney and Ensembl (the other/original genome browser depending on if you are a UCSC junkie) have started blogging a bit more about what is going on under the proverbial hood over there in Hinxton.  There are some great nuggets talking about what are some of the current problems.  These bite-sized comments should be a great glimpse into what is going on without drowning in the deluge that is ensembl-dev.   This is a recent post on the challenges of gene annotation coordination among "manual" and "automated" annotation of gene structure of groups at the same institution.   Scale that up among multiple genomes, genome centers, quality of prediction programs and assemblies, and you can see why the fungal genome comparisons could use a little bit more help. It is great to hear what ... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1368869 Sun, 13 Apr 2008 03:00:48 +0100 1368869 http://www.medworm.com/index.php?rid=1344499&cid=t_104849_125_f&fid=36046&url=http%3A%2F%2Fdentistrylibrary.blogspot.com%2F2008%2F04%2Fdatabases-on-trial.html The following two databases are currently on trial at the University of Sydney Library. Please try them out and let us know what you think using the the database evaluation forms below.FirstConsult trial - Trial ends 17th of June, 2008Integrated into our existing MDConsult subscription. This is an evidence-based clinical information tool enabling differential diagnosis, evaluation and management of medical conditions, patient education and procedure skills review.To trial POCKETConsult on your PDA:Create a personal account in MDConsultClick My PDACreate new POCKET Consult account.Once you are registered, you can download material from MDConsult and from within FirstConsult.Please fill out the Database Evaluation FormProceduresConsult - Trial ends 17th of June, 2008.This covers the procedur... DentistryLibrary@Sydney blogs http://www.medworm.com/rss/comments.php?id=1344499 Wed, 02 Apr 2008 03:36:00 +0100 1344499 http://www.medworm.com/index.php?rid=1321122&cid=t_104849_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F256148742%2F Tom Bruns, Martin Bidartondo and 250 others sent a letter to Science describing the current problems with fixing annotation in GenBank. There is an entertaining accompanying news article that interviews several people about the problem of updating annotation and species assigned to sequences in the database. In particular the problem for mycologists that many fungi found from metagenomic approaches are only identified through molecular sequences and having the wrong species associated with a sequence can be difficult when studying community ecology composition.  This problem is not limited to fungi by any means, but recent reports find as many as 20% of fungal Intergenic Spacer (ITS) sequences are mis-attributed to the wrong species. There's a nice quote in the news article from Ste... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1321122 Sat, 22 Mar 2008 18:29:19 +0100 1321122 http://www.medworm.com/index.php?rid=1546729&cid=t_104849_132_f&fid=35004&url=http%3A%2F%2Fwww.bioinformaticszen.com%2F2008%2F03%2Fbioruby-and-ruby-on-rails%2F A common practice in any computationally based field is writing code where the intended functionality has already been produced by someone else. This is usually called reinventing the wheel. This isn’t very useful since you’re spending time on an intermediate step, when instead you can use existing code and jump ahead to the next step in your research. Of course, it’s easy for me to shout bad practice on my blog, but I’m the worst person for doing this. I work in bioinformatics because I like writing code to solve problems, and my first response is to start coding, rather than look to see if someone has created a solution already. On the other hand, the benefit of using existing libraries is that you can build new things on what has already been done. BioRuby on Ra... Bioinformatics Zen blogs http://www.medworm.com/rss/comments.php?id=1546729 Thu, 06 Mar 2008 19:38:55 +0100 1546729 http://www.medworm.com/index.php?rid=1276043&cid=t_104849_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F245144266%2F I've been too busy to post much these last few days, but here are a few links to some papers I found interesting in my recent browsing. FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds - so a database of these enzymes from several different fungi including some of the white rot fungi. I'll be curious to see how the brown rot fungus Postia's genome complement compares. Evolution of host resistance in a toxin-producing bacterial–fungal alliance. Some more fungal-bacterial symbosis work in Rhizopus that follows on previous work that shows that the bacterial make a toxin that is anti-mitotic, so how does this not affect the host fungus? The authors use a... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1276043 Mon, 03 Mar 2008 23:45:22 +0100 1276043 http://www.medworm.com/index.php?rid=1223724&cid=t_104849_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F233360453%2F The UniProtKB/Swiss-Prot team is curating fungal proteins in their databases and reportedly have curated more than 20,000 fungal proteins in Release 54.8 of 05-Feb-2008. © Jason Stajich for Fungal Genomes and Comparative Genomics, 2008. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under bioinformatics, database, fungi, genome, genome annotation, genome sequencing, news. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1223724 Mon, 11 Feb 2008 22:42:37 +0100 1223724 http://www.medworm.com/index.php?rid=1216588&cid=t_104849_117_f&fid=36026&url=http%3A%2F%2Fblog.healthtalk.com%2Fzimney%2Fhawthorne-for-heart-failure-good-news-and-bad-news%2F If you are an advocate of using natural remedies and you suffer from chronic heart failure, there’s good news on the beneficial effects of the herbal extract hawthorn. A recent analysis of 14 double-blind, randomized, placebo-controlled clinical studies (the best types of medical studies available) found that oral preparations using hawthorn leaf and flower extracts improved both symptoms and heart function in patients with chronic heart failure. But before you rush off to the pharmacy or use the Internet to order hawthorn products, please bear in mind the following facts: • Chronic heart failure is an extremely serious medical condition that requires careful diagnosis, ongoing monitoring and complex medical therapy • Most of the people in the 14 medical studies were receiving hawtho... Dr. Z's Medical Report blogs http://www.medworm.com/rss/comments.php?id=1216588 Thu, 07 Feb 2008 22:09:39 +0100 1216588 http://www.medworm.com/index.php?rid=1207316&cid=t_104849_109_f&fid=34750&url=http%3A%2F%2Fpsychcentral.com%2Fblog%2Farchives%2F2008%2F02%2F05%2Fonline-support-groups-for-health-concerns%2F I’m not sure how or why this is “news” in today’s Washington Post, but apparently patients are logging on to the Internet to get emotional support and exchange information about their health (and mental health) concerns. Who would’ve thunk it? The Philadelphia Inquirer, for one, who wrote a very similar article in 1995 (yes, that was 12 years ago). The personal stories in the article are good, and it helps you realize how people are still discovering that the Internet can be a wonderful, supportive resource beyond reading the latest on your favorite celebrity or sports scores. It helps promote the fact that millions of people throughout the world have turned to the Internet for such online health support. But I do have to wonder at how much research the rep... World of Psychology blogs http://www.medworm.com/rss/comments.php?id=1207316 Tue, 05 Feb 2008 16:59:50 +0100 1207316 http://www.medworm.com/index.php?rid=1161036&cid=t_104849_132_f&fid=35001&url=http%3A%2F%2Fwww.nodalpoint.org%2F2008%2F01%2F18%2Fone_thousand_databases_high_and_rising Well it's that time of year again. The 15th annual stamp collecting edition of Nucleic Acids Research, also known as the 2008 Database issue [1], was published earlier this week. This year there are 1078 databases listed in the collection, 110 more than the previous one (see Figure 1). As we pass the one thousand databases mark (1kDB) I wonder, what proportion of the data in these databases will never be used? read more (Source: nodalpoint.org - A bioinformatics weblog) nodalpoint.org - A bioinformatics weblog blogs http://www.medworm.com/rss/comments.php?id=1161036 Fri, 18 Jan 2008 13:08:37 +0100 1161036 http://www.medworm.com/index.php?rid=1133913&cid=t_104849_133_f&fid=35096&url=http%3A%2F%2Ffeeds.b5media.com%2F%7Er%2Fb5media%2FAutismVox%2F%7E3%2F212737757%2F Exposure to thimerosal, a preservative that contains ethylmercury, during childhood is not a primary cause of autism. This is the conclusion of a study published in the January Archives of General Psychiatry (Vol. 65, no. 1) by Robert Schechter, MD, MSc, Immunization Branch and California Center for Autism and Developmental Disabilities, Research and Epidemiology, and Judith K. Grether, PhD, Environmental Health Investigations Branch, of the California Department of Public Health, Richmond. Schechter’s and Grether’s article is entitled Continuing Increases in Autism Reported to California’s Developmental Services System: Mercury in Retrograde. By studying time trends in the (Source: Autism Vox) Autism Vox blogs http://www.medworm.com/rss/comments.php?id=1133913 Tue, 08 Jan 2008 00:01:02 +0100 1133913 http://www.medworm.com/index.php?rid=1067726&cid=t_104849_109_f&fid=34750&url=http%3A%2F%2Fpsychcentral.com%2Fblog%2Farchives%2F2007%2F12%2F03%2Fthe-next-adhd-sensory-processing-disorder%2F Have you heard about sensory processing disorder (SPD)? Neither had I until I read this article in the most recent issue of Time Magazine. It’s no wonder… In PsycINFO, the psychological research database, only 29 citations were noted for this disorder, while MEDLINE found 8 articles for “sensory integration dysfunction” (another common term to reference this concern). Not all of the citations were studies (some were book chapters, book reviews, dissertations and foreign-language journal articles). One of the studies in PsycINFO was a review paper published in the Journal of Optometric Vision Development, suggesting that “delayed vestibular maturation correlates significantly with sensory integration dysfunctions” (Solan, 2007). So there may be at least ... World of Psychology blogs http://www.medworm.com/rss/comments.php?id=1067726 Mon, 03 Dec 2007 22:47:37 +0100 1067726 http://www.medworm.com/index.php?rid=1058441&cid=t_104849_150_f&fid=35777&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FPharmalot%2F%7E3%2F192350233%2F The former FDA commish yesterday praised a recently enacted plan to overhaul the way drug safety is monitored in the US, citing the recently passed FDA Amendments Act, which will create a vast new database of drug patients by 2012, CNNMoney.com reports. Such a database could prevent another debacle like Vioxx, he contended, and major health care organizations such as eHealth Initiative, Partners Healthcare and Kaiser Permanente will coordinate with insurers like Unitedhealth Group and Wellpoint, to gather and collate the data from patients. McClellan sees the info as being more complete and more objective. “If they work together and follow the same rules (in how they define adverse events and how they use the data), then you’ve got tens of millions (of people) in the database,&... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=1058441 Thu, 29 Nov 2007 11:25:01 +0100 1058441 http://www.medworm.com/index.php?rid=1024316&cid=t_104849_131_f&fid=35005&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Ffungalcompgenomics%2F%7E3%2F184281770%2F Robin reviews recent Nature paper by Ilan Wapinski et al describing the orthogroups they built from multiple fungal genomes. I've been remiss in reviewing the paper myself, but they've created an important resource in the SYNERGY tool for orthology identification and a database of orthologs of some ascomycete fungi. I am excited there is a level of interest in the properties of gene duplication and how this may be an important aspect of adaptation and evolution. The Cornell Mushroom blog has a nice treatment of the maize pathogen and Mexican delicacy Ustilago maydis corn smut. Chris and Tom took some more Coprinus pictures while I was away from the lab. © Jason Stajich for Fungal Genomes and Comparative Genomics, 2007. | Permalink | No comment Add to del.icio.us Search blo... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=1024316 Tue, 13 Nov 2007 19:56:28 +0100 1024316 http://www.medworm.com/index.php?rid=1147427&cid=t_104849_107_f&fid=36698&url=http%3A%2F%2Fminingdrugs.blogspot.com%2F2007%2F10%2Funiprot-over-billion-protein-database.html As posted by Eric Jain (via Egon) are now more than a billion RDF available.The latest release of the UniProt protein database contains just over abillion triples*! PRESS RELEASE :-)The data is all available via the (Semantic or otherwise) Web:http://beta.uniprot.org/...or can be bulk-downloaded from:ftp://ftp.uniprot.org/* Counting some reification statements, and assuming no overlap between"named graphs".P.S. This should be the last you'll hear from me on this topic -- I'm offto new adventures...Furthermore is it notable thatThe UniProt Knowledgebase (UniProtKB) and NCBI Reference Sequence (RefSeq) in conjunction with Entrez Gene are widely used resources for protein information, including function, classification and cross-references. Prior efforts in ID mapping (iProClass ID mapping ta... Mining Drug Space blogs http://www.medworm.com/rss/comments.php?id=1147427 Wed, 24 Oct 2007 23:39:00 +0100 1147427 http://www.medworm.com/index.php?rid=958991&cid=t_104849_150_f&fid=35777&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FPharmalot%2F%7E3%2F171287598%2F Last week, we wrote about Lilly’s approach to its policy concerning clinical trial disclosures. The impetus was a recent speech by the drugmaker’s ceo, Sid Taurel, who maintained that all trial results are posted on a registry on the Lilly web site. And we pointed out an inconsistency regarding the Cialis erectile dysfunction med - Lilly boasts about results of 22 trials, but has so far posted just two and plans to, ultimately, post 15. And the others? Those won’t be posted because the trials were conducted by ICOS, a company Lilly bought this year. Now, it appears we have another inconsistency - Phase IV trials completed before July 1, 2004 aren’t posted. Why that date? That’s when Lilly implemented its policy, which says the drugmaker “discloses public... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=958991 Wed, 17 Oct 2007 20:33:29 +0100 958991 http://www.medworm.com/index.php?rid=944710&cid=t_104849_150_f&fid=35777&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FPharmalot%2F%7E3%2F168440413%2F In a speech last week, Lilly ceo Sid Taurel spoke about an information revolution in healthcare and, as part of that, how health professionals and drugmakers could contribute to patient needs by making better use of data at their disposal. Toward that end, he made a point of noting how Lilly discloses clinical trial results, a hot-button issue given that the industry has been accused of failing to release unfavorable data. “Three years ago, Lilly became the first pharmaceutical company to publicly disclose the results of all (emphasis added) of our clinical trials – on the Internet. Far from harming our business in some way, I’m convinced that the increased transparency helped to improve our partnerships with researchers and to boost the confidence of doctors and patients who us... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=944710 Thu, 11 Oct 2007 13:37:44 +0100 944710 http://www.medworm.com/index.php?rid=891619&cid=t_104849_131_f&fid=35008&url=http%3A%2F%2Fscienceroll.com%2F2007%2F09%2F21%2Frecent-news-medicine-20%2F It’s been a long and hard week but I’ve been trying to keep you up-to-date about several fields of medicine, genetics and IT. Now, while watching the film Solaris (2002), I’d like to share some interesting medicine 2.0-related articles with you: 100 Web Resources for Medical Professionals: A fantastic database of resources for physicians from any kind of medical specialty. Healia Update: They launched two new search engine tools. PubMed/Medline Search is specifically designed to help consumers retrieve abstracts of scientific articles published in biomedical journals. Clinical Trials Search retrieves clinical trials information from the National Institutes of Health’s (NIH) ClinicalTrials.gov dataset. Jan at MedBlog.nl has just made it possible to search MedBlo... ScienceRoll blogs http://www.medworm.com/rss/comments.php?id=891619 Fri, 21 Sep 2007 21:25:18 +0100 891619 http://www.medworm.com/index.php?rid=888779&cid=t_104849_150_f&fid=35777&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FPharmalot%2F%7E3%2F159105395%2F The legislation making its way through Congress addresses nearly all of the controversial issues that have plagued the FDA and the pharmaceutical industry these past few years - a clinical trial database, DTC advertising, conflicts of interest on advisory panels, pediatric exclusivity and, of course, safety. But will the 427-page opus, which you can peruse right here, truly make a difference? Or were there too many compromises on some of the important issues to cause any real change in safety oversight? What do you think? Did Congress get it right? Note: There is a poll within this post, please visit the site to participate in this post’s poll. Share / E-mail (Source: Pharmalot) Pharmalot blogs http://www.medworm.com/rss/comments.php?id=888779 Thu, 20 Sep 2007 17:40:05 +0100 888779 http://www.medworm.com/index.php?rid=886439&cid=t_104849_150_f&fid=35777&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FPharmalot%2F%7E3%2F158996962%2F On the eve of congressional negotiations to pass an FDA reform bill, we asked you whether the legislation should include a provision requiring drugmakers to post their results on the Internet as part of a proposed database. The idea is controversial because drugmakers worry about competitive snooping, while those outside industry fear safety issues may be hidden. Nonetheless, the overwhelming majority of you voted in favor of disclosure. One caveat: this isn’t a scientific poll. Moreover, judging by the outcome, it would appear many industry people sat this one out. Perhaps, those of you who work for drugmakers recognized this was a losing cause? The House yesterday passed a bill that requires such a database, although the level of disclosure needs to be determined. The Senate must n... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=886439 Thu, 20 Sep 2007 11:34:53 +0100 886439 http://www.medworm.com/index.php?rid=874744&cid=t_104849_150_f&fid=35777&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FPharmalot%2F%7E3%2F156987994%2F The position against the House version of the FDA reform bill, which is labeled ‘unofficial,’ centers on three concerns - the FDA and NIH wouldn’t be able to validate the accuracy of the trial results posted; results data is too technical, and lay summaries may have too much bias, according to Consumers Union. White House opposition was first reported by Inside Health Policy (subscription required). Both House and Senate FDA reform bills require that drug trials are publicly registered, but the House bill would require a public technical trial results database, as well a lay summary of a drug trials, on the Internet. The Senate bill only calls for a study on how to create such a results registry, and gives the FDA 2-1/2 years to make it happen. A final version of the Food and... Pharmalot blogs http://www.medworm.com/rss/comments.php?id=874744 Sat, 15 Sep 2007 22:51:05 +0100 874744 http://www.medworm.com/index.php?rid=800063&cid=t_104849_87_f&fid=34867&url=http%3A%2F%2Fwww.thediabetesblog.com%2F2007%2F08%2F15%2Fthe-epidemic-is-over-exaggerated%2F Filed under: Type 2, Research, Opinion, CareIn my previous post, I looked at a RAND Corporation study of undiagnosed diabetes - something that continues to be a big problem. Now I want to zero in on one aspect of that study that really caught my eye. According to the sole author, James P. Smith, talk of a type 2 diabetes epidemic is over-exaggerated.Hang on a minute. Aren't we always hearing about the so-called epidemic proportions of diabetes' spread in the US and globally? And aren't cities like New York taking steps to track the spread of diabetes, keeping tabs on its growth just as you'd do with a contagious epidemic outbreak of, say, tuberculosis? Well, yes. But Smith isn't buying it.During the twenty-five-year period included in the study, Smith says diagnosis of men with diabetes mo... The Diabetes Blog blogs http://www.medworm.com/rss/comments.php?id=800063 Wed, 15 Aug 2007 04:00:00 +0100 800063 http://www.medworm.com/index.php?rid=765738&cid=t_104849_87_f&fid=34867&url=http%3A%2F%2Fwww.thediabetesblog.com%2F2007%2F07%2F30%2Fny-diabetes-database-raises-privacy-concerns%2F Filed under: Type 1, Type 2, Research, SupportThe New York City diabetes database, created to track the growth of (type 2) diabetes amongst the city's residents, has raised the ire of some who claim it violates their right to privacy. A reporter for the Staten Island Advance quotes resident Melissa: "Every time I go to have my blood sugar checked, my test results are being wired to the (city) Health Department. The idea of your privacy being taken away from you goes across all bounds." Melissa also says she doesn't think the city has justification to track patient records for something like diabetes, which is not contagious like, for example, tuberculosis.My first instinct on reading this: cry me a river, Melissa. Residents should be aware their blood sugar levels are being sent to the hea... The Diabetes Blog blogs http://www.medworm.com/rss/comments.php?id=765738 Mon, 30 Jul 2007 04:00:00 +0100 765738 http://www.medworm.com/index.php?rid=751682&cid=t_104849_109_f&fid=34795&url=http%3A%2F%2Fsoloshrink.blogspot.com%2F2007%2F07%2Fevernote-21-update.html EverNote®2 is offering a free, updated version of their remarkably versatile and useful note and web information collection program. It is version 2.1.0.327 which employs a new database. If you update from a previous version, your content will be saved and updated to conform to the current database engine, but it will no longer be useable with prior versions. The commercial versions of this software offer extensive additions to the basic free version. Web clips, graphics, e-mail, notes, handwriting, snapshots, sketches, and much more may all be recorded, many on either free or commercial versions. It is simply remarkable that so much versatility is offered in their free version. It is definitely worth a trip to the download section of the EverNote Website to compare versions and download ... Solo Shrink blogs http://www.medworm.com/rss/comments.php?id=751682 Mon, 23 Jul 2007 22:53:00 +0100 751682 http://www.medworm.com/index.php?rid=683500&cid=t_104849_140_f&fid=35457&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2FBattling-schizophrenia%2F%7E3%2F125949662%2F Warning: Division by zero in /home/schizo/public_html/wp-content/plugins/tla_59658.php on line 595 Greetings and Salutations .. Sorry for the delay in accessing this site. The nameservers have kicked in over the past weekend and this blog is now ready for new posts. I am in the final stages of testing the database, the permissions, etc etc etc. but, the more I prepare all of the other sites .. it’s going faster and faster now. Yep! We’re almost there .. and back to normal! So - please take a look around, and see if you notice anything different. I would appreciate your comments … (Q) Does this blog seem to load faster for you (Source: Battling-Schizophrenia) Battling-Schizophrenia blogs http://www.medworm.com/rss/comments.php?id=683500 Tue, 19 Jun 2007 01:18:47 +0100 683500 http://www.medworm.com/index.php?rid=551382&cid=t_104849_133_f&fid=35452&url=http%3A%2F%2Fwww.graphictruth.com%2F2007%2F04%2Fwhats-really-behind-stop-aclu-pizza.html ACLU - Real ID Pizza NightmareThe government and corporations are aggressively collecting information about your personal life and your habits. They want to track your purchases, your medical records, and even your relationships. The Bush Administration's policies, coupled with invasive new technologies, could eliminate your right to privacy completely. Please help us protect our privacy rights and prevent the Total Surveillance Society.Strangely - or perhaps not so strangely - Domino's Pizza is a major contributor to conservative campaigns, though I'm not sure if they specifically oppose the ACLU. Nonetheless, the choice of a pizza parlor being able to access your private info in order to see if they can or should sell you pizza is an all-too-possible future.With this ad, the ACLU points ... Graphictruth blogs http://www.medworm.com/rss/comments.php?id=551382 Fri, 06 Apr 2007 04:00:00 +0100 551382 http://www.medworm.com/index.php?rid=486601&cid=t_104849_131_f&fid=35005&url=http%3A%2F%2Ffungalgenomes.org%2Fblog%2F2007%2F03%2Fsgd-community-annotation%2F The Saccharomyces Genome Database has deployed a wiki for gene annotation from the community.  This should be an interesting experiment in how information can flow from the community into these databases. database, genome annotation, saccharomyces, wiki © Jason Stajich for Fungal Genomes and Comparative Genomics, 2007. | Permalink | No comment Add to del.icio.us Search blogs linking this post with Technorati Want more on these topics ? Browse the archive of posts filed under saccharomyces, database, genome annotation, wiki. (Source: Fungal Genomes and Comparative Genomics) Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=486601 Wed, 14 Mar 2007 01:00:11 +0100 486601 http://www.medworm.com/index.php?rid=486617&cid=t_104849_131_f&fid=35005&url=http%3A%2F%2Ffungalgenomes.org%2Fblog%2F2007%2F01%2Fthe-c-is-for-catalog%2F It seems intuitive enough that the size of an organism’s genome should be related to its evolutionary complexity. As a general rule, this tends to be true. But look within a class of organisms and you’ll find a great deal of genome size - also known as a C-value - variation. A newt’s genome, for example, is ten times the size of a frog’s. This discrepancy between genome size and evolutionary complexity is known as the C-value paradox and it has long captured the imagination of biologists. Genome sequencing and annotation have revealed that a great amount of an organism’s genome is non-coding, suggesting that a great deal of genetic content may be gained or lost without affecting the so-called “evolutionary complexity” of the organism (though whether th... Fungal Genomes and Comparative Genomics blogs http://www.medworm.com/rss/comments.php?id=486617 Wed, 31 Jan 2007 22:11:09 +0100 486617